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- PDB-1wcs: A mutant of Trypanosoma rangeli sialidase displaying trans-sialid... -

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Basic information

Entry
Database: PDB / ID: 1wcs
TitleA mutant of Trypanosoma rangeli sialidase displaying trans-sialidase activity
ComponentsSIALIDASENeuraminidase
KeywordsHYDROLASE / TRANS-SIALIDASE / SIALIDASE / TRYPANOSOMA CRUZI / TRYPANOSOMA RANGELI / PROTEIN ENGINEERING
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / metabolic process
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Concanavalin A-like lectin/glucanases superfamily / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 ...Trypanosome sialidase / BNR repeat-like domain / Concanavalin A-like lectin/glucanases superfamily / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTRYPANOSOMA RANGELI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsParis, G. / Ratier, L. / Amaya, M.F. / Nguyen, T. / Alzari, P.M. / Frasch, C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Sialidase Mutant Displaying Trans-Sialidase Activity
Authors: Paris, G. / Ratier, L. / Amaya, M.F. / Nguyen, T. / Alzari, P.M. / Frasch, C.
History
DepositionNov 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALIDASE


Theoretical massNumber of molelcules
Total (without water)70,0721
Polymers70,0721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.691, 94.691, 156.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SIALIDASE / Neuraminidase


Mass: 70071.922 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-660 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA RANGELI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O44049, exo-alpha-sialidase
Compound detailsENGINEERED RESIDUES CHAIN A, MET 118 VAL, ALA 120 PRO, SER 142 TYR, GLY 271 TYR, GLN 306 PRO
Sequence detailsTHE AUTHORS INDICATE THAT THE SEQUENCE IN THE SEQUENCE DATABASE (UNIPROT O44049) IS INCORRECT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growpH: 7
Details: 16% PEG-8000, 50MM SODIUM CACODYLATE, 100 MM AMMONIUM SULFATE, PH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17626 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.51 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1S

1n1s


Resolution: 2.8→158.11 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.819 / SU B: 48.887 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.336 905 5.1 %RANDOM
Rwork0.244 ---
obs0.248 16895 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å20 Å2
2--2.75 Å20 Å2
3----5.51 Å2
Refinement stepCycle: LAST / Resolution: 2.8→158.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 0 0 4841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224952
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9276739
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57823.472216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87115788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2411536
X-RAY DIFFRACTIONr_chiral_restr0.0910.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22411
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23242
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.53184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74925018
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01232038
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5734.51721
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.496 63
Rwork0.292 1227
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0330.0027-2.11141.4189-0.4395.5635-0.2128-0.34-0.08030.0310.1125-0.02070.56780.41840.1003-0.19830.0724-0.0016-0.2637-0.0133-0.2245.857729.433425.6154
21.5933-0.56040.262.2314-2.85083.84410.157-0.467-0.33140.4192-0.0678-0.08960.18710.3987-0.08930.42850.3487-0.06010.7440.16730.330118.35426.077358.2581
31.0598-0.90780.55293.90870.7310.75190.7006-0.4176-0.72460.3045-0.75140.28480.84980.07480.05070.69190.3801-0.03460.49450.14230.459319.2509-0.546737.4015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 376
2X-RAY DIFFRACTION2A423 - 634
3X-RAY DIFFRACTION3A377 - 422

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